Experiments

Searchable full-text extractions: founding hypothesis, core claims, experimental setups, key results and statistics — pulled out of each paper as structure. Search a cell line, an assay or an entity (e.g. HUH7) and find every paper that worked with it. This corpus stands on its own: most entries carry no reproduction assessment (yet).

• TFAP2 paralogs facilitate chromatin access for MITF at pigmentation and cell proliferation genes.

  PMID 35580127 · PMC9159589 · PLoS genetics · 2022 · 8 claims · 8 setups

  Has reproduction · 95

  Pigmentation genes are only expressed in mitfa-expressing zebrafish melanocyte-lineage cells that also express tfap2 paralogs

  gfp+ sk-mel-28 tfap2a single-cell crispr atac-seq

• ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia.

  PMID 22955991 · PMC3431496 · Genome research · 2012 · 8 claims · 8 setups

  Has reproduction · 74

  ENCODE/modENCODE define a set of working standards and guidelines for ChIP-seq covering antibody validation, experimental replication, sequencing depth, data/metadata reporting, and data quality assessment.

  small-genome nuclear whole-cell encode chip-seq chip-chip immunoblot

• DNA Methylation Directs Polycomb-Dependent 3D Genome Re-organization in Naive Pluripotency.

  PMID 31722211 · PMC6856714 · Cell reports · 2019 · 7 claims · 6 setups

  Has reproduction · 50

  The altered 3D genome of 2i-cultured ESCs (chromatin decompaction and loss of polycomb interactions at polycomb targets) is due to redistribution of polycomb away from its targets.

  ring1b− e3.5 e14 3b3l fluorescence fish situ

• Temporal control of progenitor competence shapes maturation in GABAergic neuron development in mice.

  PMID 40629142 · PMC12321585 · Nature neuroscience · 2025 · 8 claims · 8 setups

  Has reproduction · 82

  Ganglionic eminence (ventral) progenitors maintain stable differentiation competence throughout neurogenesis, generating a consistent set of postmitotic precursor states at all stages, unlike dorsal cortical progenitors whose differentiation competence changes gradually.

  dlx5 progenitors sections cortical scrna-seq trackerseq flashtag

• The revolution of the biology of the genome.

  PMID 15040884 · PMC7091781 · Cell research · 2004 · 8 claims · 6 setups

  Full-text index only

  Polyploidization and gene duplication are the major mechanisms increasing eukaryotic genome size.

  genome drosophila schizosaccharomyces gene est mount comparative

• Reactivation of a developmentally silenced embryonic globin gene.

  PMID 34290235 · PMC8295333 · Nature communications · 2021 · 8 claims · 8 setups

  Has reproduction · 85

  In embryonic (primitive) erythroid cells, the ζ-gene lies within a ~65 kb sub-TAD of open, acetylated chromatin and physically interacts with the α-globin super-enhancer.

  primitive embryos ζ-venus atac-seq dnasei chip-seq

• Identification of the imprinted KLF14 transcription factor undergoing human-specific accelerated evolution.

  PMID 17480121 · PMC1865561 · PLoS genetics · 2007 · 7 claims · 8 setups

  Full-text index only

  KLF14 is a novel imprinted gene showing monoallelic maternal expression in embryonic and extra-embryonic tissues of both human and mouse

  embryonic fetal monochromosomal fibroblasts allele-specific rt-pcr chromatin

• Hippo signaling differentially regulates distal progenitor subpopulations and their transitional states to construct the mammalian lungs.

  PMID 41932885 · PMC13219436 · Nature communications · 2026 · 8 claims · 8 setups

  Has reproduction · 91

  A fraction (15-50%) of the distal SOX9+ tip progenitor subdomain is sufficient to direct lung outgrowth through branch bifurcation, providing a mechanism for lung size control

  lung whole-mount immunofluorescence single-cell

• Sox8 remodels the cranial ectoderm to generate the ear.

  PMID 35867760 · PMC9282420 · Proceedings of the National Academy of Sciences of the United States of America · 2022 · 8 claims · 8 setups

  Has reproduction · 100

  Sox8 sits at the top of a core transcriptional circuit (Sox8, Pax2, Lmx1a, Zbtb16) that determines otic identity

  chick bulk single-cell chipseq

• Large-scale discovery and validation of functional elements in the human genome.

  PMID 15774039 · PMC1088940 · Genome biology · 2005 · 8 claims · 8 setups

  Full-text index only

  Genome-wide tiling microarray hybridization reveals large, diverse sets of transcripts, many of which lack existing gene annotations

  liver genome yeast lines tiling computational dnase